Fig. 4.

Flowchart of KnotAli. We illustrate the steps taken moving from the input alignment to the guide structure and to the final predicted structure. Note that the Relaxed Energy Minimization step is performed once for each sequence of the alignment. There are four methods inside the Relaxed Energy Minimization, that each allow for addition of more stable and possibly competing base pairs with the base pairs of the guide structure. The lowest free energy structure found in the Relaxed Energy Minimization step is output as the predicted structure of a sequence of the alignment. Given an alignment $\mathcal{A}$ of N sequences, $S_1,S_2,\dots ,S_N$ KnotAli outputs N structures $R_1,R_2,\dots ,R_N$